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Nagagaki Y, Kozakura Y, Mahandaran T, Fumoto Y, Nakato R, Shirahige K, Ishikawa F. Histone H3.3 chaperone HIRA renders stress-responsive genes poised for prospective lethal stresses in acquired tolerance. Genes Cells 2024; 29:722-734. [PMID: 38977420 DOI: 10.1111/gtc.13140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 07/10/2024]
Abstract
Appropriate responses to environmental challenges are imperative for the survival of all living organisms. Exposure to low-dose stresses is recognized to yield increased cellular fitness, a phenomenon termed hormesis. However, our molecular understanding of how cells respond to low-dose stress remains profoundly limited. Here we report that histone variant H3.3-specific chaperone, HIRA, is required for acquired tolerance, where low-dose heat stress exposure confers resistance to subsequent lethal heat stress. We found that human HIRA activates stress-responsive genes, including HSP70, by depositing histone H3.3 following low-dose stresses. These genes are also marked with histone H3 Lys-4 trimethylation and H3 Lys-9 acetylation, both active chromatin markers. Moreover, depletion of HIRA greatly diminished acquired tolerance, both in normal diploid fibroblasts and in HeLa cells. Collectively, our study revealed that HIRA is required for eliciting adaptive stress responses under environmental fluctuations and is a master regulator of stress tolerance.
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Affiliation(s)
- Yoshikazu Nagagaki
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yuji Kozakura
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Theventhiran Mahandaran
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yukiko Fumoto
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ryuichiro Nakato
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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2
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Trovato M, Bunina D, Yildiz U, Fernandez-Novel Marx N, Uckelmann M, Levina V, Perez Y, Janeva A, Garcia BA, Davidovich C, Zaugg JB, Noh KM. Histone H3.3 lysine 9 and 27 control repressive chromatin at cryptic enhancers and bivalent promoters. Nat Commun 2024; 15:7557. [PMID: 39214979 PMCID: PMC11364623 DOI: 10.1038/s41467-024-51785-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutate histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleash cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupts the deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal levels of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
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Affiliation(s)
- Matteo Trovato
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Daria Bunina
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Umut Yildiz
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Michael Uckelmann
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Vita Levina
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Yekaterina Perez
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Ana Janeva
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, and EMBL-Australia, Clayton, VIC, Australia
| | - Judith B Zaugg
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany
| | - Kyung-Min Noh
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany.
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Kim HJ, Szurgot MR, van Eeuwen T, Ricketts MD, Basnet P, Zhang AL, Vogt A, Sharmin S, Kaplan CD, Garcia BA, Marmorstein R, Murakami K. Structure of the Hir histone chaperone complex. Mol Cell 2024; 84:2601-2617.e12. [PMID: 38925115 PMCID: PMC11338637 DOI: 10.1016/j.molcel.2024.05.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/24/2024] [Accepted: 05/31/2024] [Indexed: 06/28/2024]
Abstract
The evolutionarily conserved HIRA/Hir histone chaperone complex and ASF1a/Asf1 co-chaperone cooperate to deposit histone (H3/H4)2 tetramers on DNA for replication-independent chromatin assembly. The molecular architecture of the HIRA/Hir complex and its mode of histone deposition have remained unknown. Here, we report the cryo-EM structure of the S. cerevisiae Hir complex with Asf1/H3/H4 at 2.9-6.8 Å resolution. We find that the Hir complex forms an arc-shaped dimer with a Hir1/Hir2/Hir3/Hpc2 stoichiometry of 2/4/2/4. The core of the complex containing two Hir1/Hir2/Hir2 trimers and N-terminal segments of Hir3 forms a central cavity containing two copies of Hpc2, with one engaged by Asf1/H3/H4, in a suitable position to accommodate a histone (H3/H4)2 tetramer, while the C-terminal segments of Hir3 harbor nucleic acid binding activity to wrap DNA around the Hpc2-assisted histone tetramer. The structure suggests a model for how the Hir/Asf1 complex promotes the formation of histone tetramers for their subsequent deposition onto DNA.
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Affiliation(s)
- Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mary R Szurgot
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Trevor van Eeuwen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - M Daniel Ricketts
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pratik Basnet
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Athena L Zhang
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Austin Vogt
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Samah Sharmin
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Kenji Murakami
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Vogt A, Szurgot M, Gardner L, Schultz DC, Marmorstein R. HIRA complex deposition of histone H3.3 is driven by histone tetramerization and histone-DNA binding. J Biol Chem 2024; 300:107604. [PMID: 39059488 DOI: 10.1016/j.jbc.2024.107604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Revised: 07/15/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The HIRA histone chaperone complex is comprised of four protein subunits: HIRA, UBN1, CABIN1, and transiently associated ASF1a. All four subunits have been demonstrated to play a role in the deposition of the histone variant H3.3 onto areas of actively transcribed euchromatin in cells. The mechanism by which these subunits function together to drive histone deposition has remained poorly understood. Here we present biochemical and biophysical data supporting a model whereby ASF1a delivers histone H3.3/H4 dimers to the HIRA complex, H3.3/H4 tetramerization drives the association of two HIRA/UBN1 complexes, and the affinity of the histones for DNA drives release of ASF1a and subsequent histone deposition. These findings have implications for understanding how other histone chaperone complexes may mediate histone deposition.
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Affiliation(s)
- Austin Vogt
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Mary Szurgot
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - Lauren Gardner
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA
| | - David C Schultz
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronen Marmorstein
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Center, Perelman School of Medicine at the University of Pennsylvania, Pennsylvania, USA.
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5
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D'Antona S, Porro D, Gallivanone F, Bertoli G. Characterization of cell cycle, inflammation, and oxidative stress signaling role in non-communicable diseases: Insights into genetic variants, microRNAs and pathways. Comput Biol Med 2024; 174:108346. [PMID: 38581999 DOI: 10.1016/j.compbiomed.2024.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 02/16/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Non-Communicable Diseases (NCDs) significantly impact global health, contributing to over 70% of premature deaths, as reported by the World Health Organization (WHO). These diseases have complex and multifactorial origins, involving genetic, epigenetic, environmental and lifestyle factors. While Genome-Wide Association Study (GWAS) is widely recognized as a valuable tool for identifying variants associated with complex phenotypes; the multifactorial nature of NCDs necessitates a more comprehensive exploration, encompassing not only the genetic but also the epigenetic aspect. For this purpose, we employed a bioinformatics-multiomics approach to examine the genetic and epigenetic characteristics of NCDs (i.e. colorectal cancer, coronary atherosclerosis, squamous cell lung cancer, psoriasis, type 2 diabetes, and multiple sclerosis), aiming to identify novel biomarkers for diagnosis and prognosis. Leveraging GWAS summary statistics, we pinpointed Single Nucleotide Polymorphisms (SNPs) independently associated with each NCD. Subsequently, we identified genes linked to cell cycle, inflammation and oxidative stress mechanisms, revealing shared genes across multiple diseases, suggesting common functional pathways. From an epigenetic perspective, we identified microRNAs (miRNAs) with regulatory functions targeting these genes of interest. Our findings underscore critical genetic pathways implicated in these diseases. In colorectal cancer, the dysregulation of the "Cytokine Signaling in Immune System" pathway, involving LAMA5 and SMAD7, regulated by Hsa-miR-21-5p, Hsa-miR-103a-3p, and Hsa-miR-195-5p, emerged as pivotal. In coronary atherosclerosis, the pathway associated with "binding of TCF/LEF:CTNNB1 to target gene promoters" displayed noteworthy implications, with the MYC factor controlled by Hsa-miR-16-5p as a potential regulatory factor. Squamous cell lung carcinoma analysis revealed significant pathways such as "PTK6 promotes HIF1A stabilization," regulated by Hsa-let-7b-5p. In psoriasis, the "Endosomal/Vacuolar pathway," involving HLA-C and Hsa-miR-148a-3p and Hsa-miR-148b-3p, was identified as crucial. Type 2 Diabetes implicated the "Regulation of TP53 Expression" pathway, controlled by Hsa-miR-106a-5p and Hsa-miR-106b-5p. In conclusion, our study elucidates the genetic framework and molecular mechanisms underlying NCDs, offering crucial insights into potential genetic/epigenetic biomarkers for diagnosis and prognosis. The specificity of pathways and related miRNAs in different pathologies highlights promising candidates for further clinical validation, with the potential to advance personalized treatments and alleviate the global burden of NCDs.
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Affiliation(s)
- Salvatore D'Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Francesca Gallivanone
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy
| | - Gloria Bertoli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Via F.lli Cervi 93, 20054, Milan, Italy; National Biodiversity Future Center (NBFC), Palermo, Italy.
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6
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Ignatyeva M, Patel AKM, Ibrahim A, Albiheyri RS, Zari AT, Bahieldin A, Bronner C, Sabir JSM, Hamiche A. Identification and Characterization of HIRIP3 as a Histone H2A Chaperone. Cells 2024; 13:273. [PMID: 38334665 PMCID: PMC10854748 DOI: 10.3390/cells13030273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/10/2024] Open
Abstract
HIRIP3 is a mammalian protein homologous to the yeast H2A.Z deposition chaperone Chz1. However, the structural basis underlying Chz's binding preference for H2A.Z over H2A, as well as the mechanism through which Chz1 modulates histone deposition or replacement, remains enigmatic. In this study, we aimed to characterize the function of HIRIP3 and to identify its interacting partners in HeLa cells. Our findings reveal that HIRIP3 is specifically associated in vivo with H2A-H2B dimers and CK2 kinase. While bacterially expressed HIRIP3 exhibited a similar binding affinity towards H2A and H2A.Z, the associated CK2 kinase showed a notable preference for H2A phosphorylation at serine 1. The recombinant HIRIP3 physically interacted with the H2A αC helix through an extended CHZ domain and played a crucial role in depositing the canonical core histones onto naked DNA. Our results demonstrate that mammalian HIRIP3 acts as an H2A histone chaperone, assisting in its selective phosphorylation by Ck2 kinase at serine 1 and facilitating its deposition onto chromatin.
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Affiliation(s)
- Maria Ignatyeva
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IG-BMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France (A.I.); (C.B.)
| | - Abdul Kareem Mohideen Patel
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IG-BMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France (A.I.); (C.B.)
| | - Abdulkhaleg Ibrahim
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IG-BMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France (A.I.); (C.B.)
| | - Raed S. Albiheyri
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.S.A.); (A.T.Z.); (A.B.)
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ali T. Zari
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.S.A.); (A.T.Z.); (A.B.)
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.S.A.); (A.T.Z.); (A.B.)
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Christian Bronner
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IG-BMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France (A.I.); (C.B.)
| | - Jamal S. M. Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.S.A.); (A.T.Z.); (A.B.)
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IG-BMC), CNRS UMR7104, INSERM U964, Université de Strasbourg, 67404 Illkirch, France (A.I.); (C.B.)
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (R.S.A.); (A.T.Z.); (A.B.)
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7
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Hao H, Ren C, Lian Y, Zhao M, Bo T, Xu J, Wang W. Independent and Complementary Functions of Caf1b and Hir1 for Chromatin Assembly in Tetrahymena thermophila. Cells 2023; 12:2828. [PMID: 38132148 PMCID: PMC10741905 DOI: 10.3390/cells12242828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex mediate replication-couple (RC) and replication-independent (RI) nucleosome assembly, respectively. CHAF1B and HIRA share a similar domain but play different roles in nucleosome assembly by binding to the different interactors. At present, there is limited understanding for the similarities and differences in their respective functions. Tetrahymena thermophila contains transcriptionally active polyploid macronuclei (MAC) and transcriptionally silent diploid micronuclei (MIC). Here, the distribution patterns of Caf1b and Hir1 exhibited both similarities and distinctions. Both proteins localized to the MAC and MIC during growth, and to the MIC during conjugation. However, Hir1 exhibited additional signaling on parental MAC and new MAC during sexual reproduction and displayed a punctate signal on developing anlagen. Caf1b and Hir1 only co-localized in the MIC with Pcna1 during conjugation. Knockdown of CAF1B impeded cellular growth and arrested sexual reproductive development. Loss of HIR1 led to MIC chromosome defects and aborted sexual development. Co-interference of CAF1B and HIR1 led to a more severe phenotype. Moreover, CAF1B knockdown led to the up-regulation of HIR1 expression, while knockdown of HIR1 also led to an increase in CAF1B expression. Furthermore, Caf1b and Hir1 interacted with different interactors. These results showed that CAF-1 and Hir1 have independent and complementary functions for chromatin assembly in T. thermophila.
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Affiliation(s)
- Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Chenhui Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Min Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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8
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Delaney K, Weiss N, Almouzni G. The cell-cycle choreography of H3 variants shapes the genome. Mol Cell 2023; 83:3773-3786. [PMID: 37734377 PMCID: PMC10621666 DOI: 10.1016/j.molcel.2023.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/07/2023] [Accepted: 08/29/2023] [Indexed: 09/23/2023]
Abstract
Histone variants provide versatility in the basic unit of chromatin, helping to define dynamic landscapes and cell fates. Maintaining genome integrity is paramount for the cell, and it is intimately linked with chromatin dynamics, assembly, and disassembly during DNA transactions such as replication, repair, recombination, and transcription. In this review, we focus on the family of H3 variants and their dynamics in space and time during the cell cycle. We review the distinct H3 variants' specific features along with their escort partners, the histone chaperones, compiled across different species to discuss their distinct importance considering evolution. We place H3 dynamics at different times during the cell cycle with the possible consequences for genome stability. Finally, we examine how their mutation and alteration impact disease. The emerging picture stresses key parameters in H3 dynamics to reflect on how when they are perturbed, they become a source of stress for genome integrity.
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Affiliation(s)
- Kamila Delaney
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Nicole Weiss
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS, Sorbonne Université, Nuclear Dynamics Unit, Equipe Labellisée Ligue contre le Cancer, 26 rue d'Ulm, 75005 Paris, France.
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9
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Gal C, Cochrane GA, Morgan BA, Rallis C, Bähler J, Whitehall SK. The longevity and reversibility of quiescence in Schizosaccharomyces pombe are dependent upon the HIRA histone chaperone. Cell Cycle 2023; 22:1921-1936. [PMID: 37635373 PMCID: PMC10599175 DOI: 10.1080/15384101.2023.2249705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/04/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Quiescence (G0) is a reversible non-dividing state that facilitates cellular survival in adverse conditions. Here, we demonstrate that the HIRA histone chaperone complex is required for the reversibility and longevity of nitrogen starvation-induced quiescence in Schizosaccharomyces pombe. The HIRA protein, Hip1 is not required for entry into G0 or the induction of autophagy. Although hip1Δ cells retain metabolic activity in G0, they rapidly lose the ability to resume proliferation. After a short period in G0 (1 day), hip1Δ mutants can resume cell growth in response to the restoration of a nitrogen source but do not efficiently reenter the vegetative cell cycle. This correlates with a failure to induce the expression of MBF transcription factor-dependent genes that are critical for S phase. In addition, hip1Δ G0 cells rapidly progress to a senescent state in which they can no longer re-initiate growth following nitrogen source restoration. Analysis of a conditional hip1 allele is consistent with these findings and indicates that HIRA is required for efficient exit from quiescence and prevents an irreversible cell cycle arrest.
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Affiliation(s)
- Csenge Gal
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Grace A. Cochrane
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Brian A. Morgan
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Charalampos Rallis
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Jürg Bähler
- Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, UK
| | - Simon K. Whitehall
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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10
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McPherson JME, Grossmann LC, Salzler HR, Armstrong RL, Kwon E, Matera AG, McKay DJ, Duronio RJ. Reduced histone gene copy number disrupts Drosophila Polycomb function. Genetics 2023; 224:iyad106. [PMID: 37279945 PMCID: PMC10411577 DOI: 10.1093/genetics/iyad106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/08/2023] Open
Abstract
The chromatin of animal cells contains two types of histones: canonical histones that are expressed during S phase of the cell cycle to package the newly replicated genome, and variant histones with specialized functions that are expressed throughout the cell cycle and in non-proliferating cells. Determining whether and how canonical and variant histones cooperate to regulate genome function is integral to understanding how chromatin-based processes affect normal and pathological development. Here, we demonstrate that variant histone H3.3 is essential for Drosophila development only when canonical histone gene copy number is reduced, suggesting that coordination between canonical H3.2 and variant H3.3 expression is necessary to provide sufficient H3 protein for normal genome function. To identify genes that depend upon, or are involved in, this coordinate regulation we screened for heterozygous chromosome 3 deficiencies that impair development of flies bearing reduced H3.2 and H3.3 gene copy number. We identified two regions of chromosome 3 that conferred this phenotype, one of which contains the Polycomb gene, which is necessary for establishing domains of facultative chromatin that repress master regulator genes during development. We further found that reduction in Polycomb dosage decreases viability of animals with no H3.3 gene copies. Moreover, heterozygous Polycomb mutations result in de-repression of the Polycomb target gene Ubx and cause ectopic sex combs when either canonical or variant H3 gene copy number is reduced. We conclude that Polycomb-mediated facultative heterochromatin function is compromised when canonical and variant H3 gene copy number falls below a critical threshold.
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Affiliation(s)
- Jeanne-Marie E McPherson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lucy C Grossmann
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Harmony R Salzler
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Esther Kwon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - A Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel J McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
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11
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Palukuri MV, Patil RS, Marcotte EM. Molecular complex detection in protein interaction networks through reinforcement learning. BMC Bioinformatics 2023; 24:306. [PMID: 37532987 PMCID: PMC10394916 DOI: 10.1186/s12859-023-05425-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND Proteins often assemble into higher-order complexes to perform their biological functions. Such protein-protein interactions (PPI) are often experimentally measured for pairs of proteins and summarized in a weighted PPI network, to which community detection algorithms can be applied to define the various higher-order protein complexes. Current methods include unsupervised and supervised approaches, often assuming that protein complexes manifest only as dense subgraphs. Utilizing supervised approaches, the focus is not on how to find them in a network, but only on learning which subgraphs correspond to complexes, currently solved using heuristics. However, learning to walk trajectories on a network to identify protein complexes leads naturally to a reinforcement learning (RL) approach, a strategy not extensively explored for community detection. Here, we develop and evaluate a reinforcement learning pipeline for community detection on weighted protein-protein interaction networks to detect new protein complexes. The algorithm is trained to calculate the value of different subgraphs encountered while walking on the network to reconstruct known complexes. A distributed prediction algorithm then scales the RL pipeline to search for novel protein complexes on large PPI networks. RESULTS The reinforcement learning pipeline is applied to a human PPI network consisting of 8k proteins and 60k PPI, which results in 1,157 protein complexes. The method demonstrated competitive accuracy with improved speed compared to previous algorithms. We highlight protein complexes such as C4orf19, C18orf21, and KIAA1522 which are currently minimally characterized. Additionally, the results suggest TMC04 be a putative additional subunit of the KICSTOR complex and confirm the involvement of C15orf41 in a higher-order complex with HIRA, CDAN1, ASF1A, and by 3D structural modeling. CONCLUSIONS Reinforcement learning offers several distinct advantages for community detection, including scalability and knowledge of the walk trajectories defining those communities. Applied to currently available human protein interaction networks, this method had comparable accuracy with other algorithms and notable savings in computational time, and in turn, led to clear predictions of protein function and interactions for several uncharacterized human proteins.
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Affiliation(s)
- Meghana V Palukuri
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
- Oden Institute for Computational Engineering and Sciences, University of Texas, Austin, TX, 78712, USA.
| | - Ridhi S Patil
- Department of Biomedical Engineering, University of Texas, Austin, TX, 78712, USA.
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, University of Texas, Austin, TX, 78712, USA.
- Oden Institute for Computational Engineering and Sciences, University of Texas, Austin, TX, 78712, USA.
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12
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Olan I, Handa T, Narita M. Beyond SAHF: An integrative view of chromatin compartmentalization during senescence. Curr Opin Cell Biol 2023; 83:102206. [PMID: 37451177 DOI: 10.1016/j.ceb.2023.102206] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/27/2023] [Accepted: 05/30/2023] [Indexed: 07/18/2023]
Abstract
Cellular senescence, a persistent form of cell cycle arrest, has been linked to the formation of heterochromatic foci, accompanied by additional concentric epigenetic layers. However, senescence is a highly heterogeneous phenotype, and the formation of these structures is context dependent. Recent developments in the understanding of the high-order chromatin organization have opened new avenues for contextualizing the nuclear and chromatin phenotypes of senescence. Oncogene-induced senescence displays prominent foci and typically exhibits increased chromatin compartmentalization, based on the chromosome conformation assays, as marked by increased transcompaction and segregation of the heterochromatin and euchromatin. However, other types of senescence (e.g., replicative senescence) exhibit comparatively lower levels of compartmentalization. Thus, a more integrative view of the global rearrangement of the chromatin architecture that occurs during senescence is emerging, with potential functional implications for the heterogeneity of the senescence phenotype.
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Affiliation(s)
- Ioana Olan
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - Tetsuya Handa
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
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13
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Kleijwegt C, Bressac F, Seurre C, Bouchereau W, Cohen C, Texier P, Simonet T, Schaeffer L, Lomonte P, Corpet A. Interplay between PML NBs and HIRA for H3.3 dynamics following type I interferon stimulus. eLife 2023; 12:e80156. [PMID: 37227756 PMCID: PMC10212570 DOI: 10.7554/elife.80156] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 04/25/2023] [Indexed: 05/26/2023] Open
Abstract
Promyelocytic leukemia Nuclear Bodies (PML NBs) are nuclear membrane-less organelles physically associated with chromatin underscoring their crucial role in genome function. The H3.3 histone chaperone complex HIRA accumulates in PML NBs upon senescence, viral infection or IFN-I treatment in primary cells. Yet, the molecular mechanisms of this partitioning and its function in regulating histone dynamics have remained elusive. By using specific approaches, we identify intermolecular SUMO-SIM interactions as an essential mechanism for HIRA recruitment in PML NBs. Hence, we describe a role of PML NBs as nuclear depot centers to regulate HIRA distribution in the nucleus, dependent both on SP100 and DAXX/H3.3 levels. Upon IFN-I stimulation, PML is required for interferon-stimulated genes (ISGs) transcription and PML NBs become juxtaposed to ISGs loci at late time points of IFN-I treatment. HIRA and PML are necessary for the prolonged H3.3 deposition at the transcriptional end sites of ISGs, well beyond the peak of transcription. Though, HIRA accumulation in PML NBs is dispensable for H3.3 deposition on ISGs. We thus uncover a dual function for PML/PML NBs, as buffering centers modulating the nuclear distribution of HIRA, and as chromosomal hubs regulating ISGs transcription and thus HIRA-mediated H3.3 deposition at ISGs upon inflammatory response.
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Affiliation(s)
- Constance Kleijwegt
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Florent Bressac
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Coline Seurre
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Wilhelm Bouchereau
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Camille Cohen
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Pascale Texier
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Thomas Simonet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Laurent Schaeffer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, Institut NeuroMyoGène (INMG), team Nerve-Muscle interactionsLyonFrance
| | - Patrick Lomonte
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
| | - Armelle Corpet
- University of Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) laboratory, team Chromatin Dynamics, Nuclear Domains, VirusLyonFrance
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14
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Nabeel-Shah S, Garg J, Ashraf K, Jeyapala R, Lee H, Petrova A, Burns JD, Pu S, Zhang Z, Greenblatt JF, Pearlman RE, Lambert JP, Fillingham J. Multilevel interrogation of H3.3 reveals a primordial role in transcription regulation. Epigenetics Chromatin 2023; 16:10. [PMID: 37024975 PMCID: PMC10080907 DOI: 10.1186/s13072-023-00484-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/28/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Eukaryotic cells can rapidly adjust their transcriptional profile in response to molecular needs. Such dynamic regulation is, in part, achieved through epigenetic modifications and selective incorporation of histone variants into chromatin. H3.3 is the ancestral H3 variant with key roles in regulating chromatin states and transcription. Although H3.3 has been well studied in metazoans, information regarding the assembly of H3.3 onto chromatin and its possible role in transcription regulation remain poorly documented outside of Opisthokonts. RESULTS We used the nuclear dimorphic ciliate protozoan, Tetrahymena thermophila, to investigate the dynamics of H3 variant function in evolutionarily divergent eukaryotes. Functional proteomics and immunofluorescence analyses of H3.1 and H3.3 revealed a highly conserved role for Nrp1 and Asf1 histone chaperones in nuclear influx of histones. Cac2, a putative subunit of H3.1 deposition complex CAF1, is not required for growth, whereas the expression of the putative ortholog of the H3.3-specific chaperone Hir1 is essential in Tetrahymena. Our results indicate that Cac2 and Hir1 have distinct localization patterns during different stages of the Tetrahymena life cycle and suggest that Cac2 might be dispensable for chromatin assembly. ChIP-seq experiments in growing Tetrahymena show H3.3 enrichment over the promoters, gene bodies, and transcription termination sites of highly transcribed genes. H3.3 knockout followed by RNA-seq reveals large-scale transcriptional alterations in functionally important genes. CONCLUSION Our results provide an evolutionary perspective on H3.3's conserved role in maintaining the transcriptional landscape of cells and on the emergence of specialized chromatin assembly pathways.
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Affiliation(s)
- Syed Nabeel-Shah
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Jyoti Garg
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Kanwal Ashraf
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Renu Jeyapala
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
| | - Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, Canada
| | - Alexandra Petrova
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada
| | - James D Burns
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Shuye Pu
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
- Department of Computer Science, University of Toronto, Toronto, M5S 1A8, Canada
| | - Jack F Greenblatt
- Donnelly Centre, University of Toronto, Toronto, M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, M5S 1A8, Canada
| | - Ronald E Pearlman
- Department of Biology, York University, 4700 Keele St, Toronto, M3J 1P3, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Cancer Research Center, Big Data Research Center, Université Laval, Quebec City, QC, Canada
- CHU de Québec Research Center, CHUL, 2705 Laurier Boulevard, Quebec City, QC, Canada
| | - Jeffrey Fillingham
- Department of Chemistry and Biology, Toronto Metropolitan University, 350 Victoria St, Toronto, M5B 2K3, Canada.
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15
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McPherson JME, Grossmann LC, Armstrong RL, Kwon E, Salzler HR, Matera AG, McKay DJ, Duronio RJ. Reduced histone gene copy number disrupts Drosophila Polycomb function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534544. [PMID: 37034607 PMCID: PMC10081267 DOI: 10.1101/2023.03.28.534544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The chromatin of animal cells contains two types of histones: canonical histones that are expressed during S phase of the cell cycle to package the newly replicated genome, and variant histones with specialized functions that are expressed throughout the cell cycle and in non-proliferating cells. Determining whether and how canonical and variant histones cooperate to regulate genome function is integral to understanding how chromatin-based processes affect normal and pathological development. Here, we demonstrate that variant histone H3.3 is essential for Drosophila development only when canonical histone gene copy number is reduced, suggesting that coordination between canonical H3.2 and variant H3.3 expression is necessary to provide sufficient H3 protein for normal genome function. To identify genes that depend upon, or are involved in, this coordinate regulation we screened for heterozygous chromosome 3 deficiencies that impair development of flies bearing reduced H3.2 and H3.3 gene copy number. We identified two regions of chromosome 3 that conferred this phenotype, one of which contains the Polycomb gene, which is necessary for establishing domains of facultative chromatin that repress master regulator genes during development. We further found that reduction in Polycomb dosage decreases viability of animals with no H3.3 gene copies. Moreover, heterozygous Polycomb mutations result in de-repression of the Polycomb target gene Ubx and cause ectopic sex combs when either canonical or variant H3 gene copy number is also reduced. We conclude that Polycomb-mediated facultative heterochromatin function is compromised when canonical and variant H3 gene copy number falls below a critical threshold.
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Affiliation(s)
- Jeanne-Marie E. McPherson
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Lucy C. Grossmann
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robin L. Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Esther Kwon
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Harmony R. Salzler
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - A. Gregory Matera
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Daniel J. McKay
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Robert J. Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, 27599 USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, 27599, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, 27599, USA
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16
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Poulet A, Rousselot E, Téletchéa S, Noirot C, Jacob Y, van Wolfswinkel J, Thiriet C, Duc C. The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. Int J Mol Sci 2023; 24:1051. [PMID: 36674565 PMCID: PMC9864664 DOI: 10.3390/ijms24021051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/07/2023] Open
Abstract
The nucleosome is composed of histones and DNA. Prior to their deposition on chromatin, histones are shielded by specialized and diverse proteins known as histone chaperones. They escort histones during their entire cellular life and ensure their proper incorporation in chromatin. Physarum polycephalum is a Mycetozoan, a clade located at the crown of the eukaryotic tree. We previously found that histones, which are highly conserved between plants and animals, are also highly conserved in Physarum. However, histone chaperones differ significantly between animal and plant kingdoms, and this thus probed us to further study the conservation of histone chaperones in Physarum and their evolution relative to animal and plants. Most of the known histone chaperones and their functional domains are conserved as well as key residues required for histone and chaperone interactions. Physarum is divergent from yeast, plants and animals, but PpHIRA, PpCABIN1 and PpSPT6 are similar in structure to plant orthologues. PpFACT is closely related to the yeast complex, and the Physarum genome encodes the animal-specific APFL chaperone. Furthermore, we performed RNA sequencing to monitor chaperone expression during the cell cycle and uncovered two distinct patterns during S-phase. In summary, our study demonstrates the conserved role of histone chaperones in handling histones in an early-branching eukaryote.
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Affiliation(s)
- Axel Poulet
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Ellyn Rousselot
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Stéphane Téletchéa
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Céline Noirot
- INRAE, UR 875 Unité de Mathématique et Informatique Appliquées, Genotoul Bioinfo Auzeville, 31326 Castanet-Tolosan, France
| | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Josien van Wolfswinkel
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, New Haven, CT 06511, USA
| | - Christophe Thiriet
- Université Rennes 1, CNRS, IGDR (Institut de Génétique et Développement de Rennes)—UMR 6290, 35043 Rennes, France
| | - Céline Duc
- Faculté des Sciences et Techniques, Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
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17
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Stilp AC, Scherer M, König P, Fürstberger A, Kestler HA, Stamminger T. The chromatin remodeling protein ATRX positively regulates IRF3-dependent type I interferon production and interferon-induced gene expression. PLoS Pathog 2022; 18:e1010748. [PMID: 35939517 PMCID: PMC9387936 DOI: 10.1371/journal.ppat.1010748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/18/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
The chromatin remodeling protein alpha thalassemia/mental retardation syndrome X-linked (ATRX) is a component of promyelocytic leukemia nuclear bodies (PML-NBs) and thereby mediates intrinsic immunity against several viruses including human cytomegalovirus (HCMV). As a consequence, viruses have evolved different mechanisms to antagonize ATRX, such as displacement from PML-NBs or degradation. Here, we show that depletion of ATRX results in an overall impaired antiviral state by decreasing transcription and subsequent secretion of type I IFNs, which is followed by reduced expression of interferon-stimulated genes (ISGs). ATRX interacts with the transcription factor interferon regulatory factor 3 (IRF3) and associates with the IFN-β promoter to facilitate transcription. Furthermore, whole transcriptome sequencing revealed that ATRX is required for efficient IFN-induced expression of a distinct set of ISGs. Mechanistically, we found that ATRX positively modulates chromatin accessibility specifically upon IFN signaling, thereby affecting promoter regions with recognition motifs for AP-1 family transcription factors. In summary, our study uncovers a novel co-activating function of the chromatin remodeling factor ATRX in innate immunity that regulates chromatin accessibility and subsequent transcription of interferons and ISGs. Consequently, ATRX antagonization by viral proteins and ATRX mutations in tumors represent important strategies to broadly compromise both intrinsic and innate immune responses. ATRX is a member of a family of chromatin remodeling proteins required for deposition of the histone variant H3.3 at specific genomic regions. This is important to maintain silencing at these sites. Furthermore, ATRX represents a component of PML nuclear bodies (PML-NBs) which are considered as enigmatic nuclear protein accumulations exhibiting a tight link to cell-intrinsic restriction of viral infections. Previous studies demonstrated that many viruses target ATRX by either displacement or degradation. So far, it is believed that this serves to alleviate ATRX-instituted silencing of viral gene expression. Our results reveal a novel and unexpectedly broad function of ATRX as a co-activator of the innate immune response. We show that ATRX is required for both DNA and RNA sensing pathways to activate interferon (IFN) gene expression as well as for upregulation of a distinct set of interferon-stimulated genes. Assessment of chromatin accessibility detected that IFN acts as a switch to regulate the function of ATRX in heterochromatin remodeling. ATRX positively modulates chromatin accessibility specifically upon IFN signaling, thereby affecting promoter regions with recognition motifs for AP-1 family transcription factors. Loss of ATRX due to viral infection or due to tumor mutations may thus broadly compromise cellular innate immunity.
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Affiliation(s)
| | - Myriam Scherer
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Patrick König
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Thomas Stamminger
- Institute of Virology, Ulm University Medical Center, Ulm, Germany
- * E-mail:
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18
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Cabin1 domain-containing gene picd-1 interacts with pry-1/Axin to regulate multiple processes in Caenorhabditis elegans. Sci Rep 2022; 12:12029. [PMID: 35835800 PMCID: PMC9283418 DOI: 10.1038/s41598-022-15873-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/30/2022] [Indexed: 11/08/2022] Open
Abstract
The Axin family of scaffolding proteins control diverse processes, such as facilitating the interactions between cellular components and providing specificity to signaling pathways. While several Axin family members have been discovered in metazoans and shown to play crucial roles, their mechanism of action are not well understood. The Caenorhabditis elegans Axin homolog, pry-1, is a powerful tool for identifying interacting genes and downstream effectors that function in a conserved manner to regulate Axin-mediated signaling. Our lab and others have established pry-1's essential role in developmental processes that affect the reproductive system, seam cells, and a posterior P lineage cell, P11.p. Additionally, pry-1 is crucial for lipid metabolism, stress responses, and aging. In this study, we expanded on our previous work on pry-1 by reporting a novel interacting gene named picd-1 (pry-1-interacting and Cabin1 domain-containing). PICD-1 protein shares sequence conservation with CABIN1, a component of the HUCA complex. Our findings have revealed that PICD-1 is involved in several pry-1-mediated processes, including stress response and lifespan maintenance. picd-1's expression overlapped with that of pry-1 in multiple tissues throughout the lifespan. Furthermore, PRY-1 and PICD-1 inhibited CREB-regulated transcriptional coactivator homolog CRTC-1, which promotes longevity in a calcineurin-dependent manner. Overall, our study has demonstrated that picd-1 is necessary for mediating pry-1 function and provides the basis to investigate whether Cabin-1 domain-containing protein plays a similar role in Axin signaling in other systems.
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Transcription-coupled H3.3 recycling: A link with chromatin states. Semin Cell Dev Biol 2022; 135:13-23. [PMID: 35595602 DOI: 10.1016/j.semcdb.2022.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/09/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022]
Abstract
Histone variant H3.3 is incorporated into chromatin throughout the cell cycle and even in non-cycling cells. This histone variant marks actively transcribed chromatin regions with high nucleosome turnover, as well as silent pericentric and telomeric repetitive regions. In the past few years, significant progress has been made in our understanding of mechanisms involved in the transcription-coupled deposition of H3.3. Here we review how, during transcription, new H3.3 deposition intermingles with the fate of the old H3.3 variant and its recycling. First, we describe pathways enabling the incorporation of newly synthesized vs old H3.3 histones in the context of transcription. We then review the current knowledge concerning differences between these two H3.3 populations, focusing on their PTMs composition. Finally, we discuss the implications of H3.3 recycling for the maintenance of the transcriptional state and underline the emerging importance of H3.3 as a potent epigenetic regulator for both maintaining and switching a transcriptional state.
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20
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Zhang M, Zhao X, Feng X, Hu X, Zhao X, Lu W, Lu X. Histone chaperone HIRA complex regulates retrotransposons in embryonic stem cells. Stem Cell Res Ther 2022; 13:137. [PMID: 35365225 PMCID: PMC8973876 DOI: 10.1186/s13287-022-02814-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 03/11/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone cell cycle regulator (HIRA) complex is an important histone chaperone that mediates the deposition of the H3.3 histone variant onto chromatin independently from DNA synthesis. However, it is still unknown whether it participates in the expression control of retrotransposons and cell fate determination. METHODS We screened the role of HIRA complex members in repressing the expression of retrotransposons by shRNA depletion in embryonic stem cells (ESCs) followed by RT-qPCR. RNA-seq was used to study the expression profiles after depletion of individual HIRA member. RT-qPCR and western blot were used to determine overexpression of HIRA complex members. Chromatin immunoprecipitation (ChIP)-qPCR was used to find the binding of H3.3, HIRA members to chromatin. Co-immunoprecipitation was used to identify the interaction between Hira mutant and Ubn2. ChIP-qPCR was used to identify H3.3 deposition change and western blot of chromatin extract was used to validate the epigenetic change. Bioinformatics analysis was applied for the analysis of available ChIP-seq data. RESULTS We revealed that Hira, Ubn2, and Ubn1 were the main repressors of 2-cell marker retrotransposon MERVL among HIRA complex members. Surprisingly, Ubn2 and Hira targeted different groups of retrotransposons and retrotransposon-derived long noncoding RNAs (lncRNAs), despite that they partially shared target genes. Furthermore, Ubn2 prevented ESCs to gain a 2-cell like state or activate trophectodermal genes upon differentiation. Mechanistically, Ubn2 and Hira suppressed retrotransposons by regulating the deposition of histone H3.3. Decreased H3.3 deposition, that was associated with the loss of Ubn2 or Hira, caused the reduction of H3K9me2 and H3K9me3, which are known repressive marks of retrotransposons. CONCLUSIONS Overall, our findings shed light on the distinct roles of HIRA complex members in controlling retrotransposons and cell fate conversion in ESCs.
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Affiliation(s)
- Miao Zhang
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xin Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Xiao Feng
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | | | - Xuan Zhao
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, People's Republic of China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300350, People's Republic of China.
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21
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Smith R, Susor A, Ming H, Tait J, Conti M, Jiang Z, Lin CJ. The H3.3 chaperone Hira complex orchestrates oocyte developmental competence. Development 2022; 149:274223. [PMID: 35112132 PMCID: PMC8959146 DOI: 10.1242/dev.200044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/16/2022] [Indexed: 11/20/2022]
Abstract
Successful reproduction requires an oocyte competent to sustain early embryo development. By the end of oogenesis, the oocyte has entered a transcriptionally silenced state, the mechanisms and significance of which remain poorly understood. Histone H3.3, a histone H3 variant, has unique cell cycle-independent functions in chromatin structure and gene expression. Here, we have characterised the H3.3 chaperone Hira/Cabin1/Ubn1 complex, showing that loss of function of any of these subunits causes early embryogenesis failure in mouse. Transcriptome and nascent RNA analyses revealed that transcription is aberrantly silenced in mutant oocytes. Histone marks, including H3K4me3 and H3K9me3, are reduced and chromatin accessibility is impaired in Hira/Cabin1 mutants. Misregulated genes in mutant oocytes include Zscan4d, a two-cell specific gene involved in zygote genome activation. Overexpression of Zscan4 in the oocyte partially recapitulates the phenotypes of Hira mutants and Zscan4 knockdown in Cabin1 mutant oocytes partially restored their developmental potential, illustrating that temporal and spatial expression of Zscan4 is fine-tuned at the oocyte-to-embryo transition. Thus, the H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and embryogenesis, through modulating chromatin condensation and transcriptional quiescence. Summary: The H3.3 chaperone Hira complex has a maternal effect function in oocyte developmental competence and embryogenesis by modulating chromatin condensation and transcriptional quiescence.
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Affiliation(s)
- Rowena Smith
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburska 89, 277 21 Libechov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Janet Tait
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Chih-Jen Lin
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
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22
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Wen T, Chen QY. Dynamic Activity of Histone H3-Specific Chaperone Complexes in Oncogenesis. Front Oncol 2022; 11:806974. [PMID: 35087762 PMCID: PMC8786718 DOI: 10.3389/fonc.2021.806974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Canonical histone H3.1 and variant H3.3 deposit at different sites of the chromatin via distinct histone chaperones. Histone H3.1 relies on chaperone CAF-1 to mediate replication-dependent nucleosome assembly during S-phase, while H3.3 variant is regulated and incorporated into the chromatin in a replication-independent manner through HIRA and DAXX/ATRX. Current literature suggests that dysregulated expression of histone chaperones may be implicated in tumor progression. Notably, ectopic expression of CAF-1 can promote a switch between canonical H3.1 and H3 variants in the chromatin, impair the chromatic state, lead to chromosome instability, and impact gene transcription, potentially contributing to carcinogenesis. This review focuses on the chaperone proteins of H3.1 and H3.3, including structure, regulation, as well as their oncogenic and tumor suppressive functions in tumorigenesis.
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Affiliation(s)
- Ting Wen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qiao Yi Chen
- Department of Cell Biology and Genetics, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
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23
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Wang S, Bai J. Functions and roles of IFIX, a member of the human HIN-200 family, in human diseases. Mol Cell Biochem 2022; 477:771-780. [PMID: 35039991 DOI: 10.1007/s11010-021-04297-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/04/2021] [Indexed: 11/25/2022]
Abstract
Pyrin and hematopoietic expression, interferon-inducible nature, and nuclear localization (HIN) domain family member 1 (PYHIN1), also known as IFIX, belongs to the family of pyrin proteins. This family includes structurally and functionally related mouse (e.g., p202, p203, and p204 proteins) and human (e.g., the interferon-inducible protein 16, absent in melanoma 2 protein, myeloid cell nuclear differentiation antigen, and pyrin and HIN domain family 1 or IFIX) proteins. The IFIX protein belongs to the HIN-200 family of interferon-inducible proteins that have a 200-amino acid signature motif at their C-termini. The increased expression of pyrin proteins in most cell types inhibits cell cycle control and modulates cell survival. Consistent with this role for pyrin proteins, IFIX is a potential antiviral DNA sensor that is essential for immune responses, the detection of viral DNA in the nucleus and cytoplasm, and the binding of foreign DNA via its HIN domain in a sequence non-specific manner. By promoting the ubiquitination and subsequent degradation of MDM2, IFIX acts as a tumor suppressor, thereby leading to p53/TP53 stabilization, HDAC1 regulation via the ubiquitin-proteasome pathway, and tumor-cell-specific silencing of the maspin gene. These data demonstrate that the potential molecular mechanism(s) underlying the action of the IFIX protein might be associated with the development of human diseases, such as viral infections, malignant tumors, and autoimmune diseases. This review summarizes the current insights into IFIX functions and how its regulation affects the outcomes of various human diseases.
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Affiliation(s)
- Shan Wang
- Department of Oral Pathology, Hospital of Stomatology, The First Affiliated Hospital, Harbin Medical University, Harbin, 150001, People's Republic of China.
| | - Jie Bai
- Department of Ophthalmology, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, People's Republic of China.
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24
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Guo P, Liu Y, Geng F, Daman AW, Liu X, Zhong L, Ravishankar A, Lis R, Durán JGB, Itkin T, Tang F, Zhang T, Xiang J, Shido K, Ding BS, Wen D, Josefowicz SZ, Rafii S. Histone variant H3.3 maintains adult haematopoietic stem cell homeostasis by enforcing chromatin adaptability. Nat Cell Biol 2022; 24:99-111. [PMID: 34961794 PMCID: PMC9166935 DOI: 10.1038/s41556-021-00795-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 10/14/2021] [Indexed: 01/25/2023]
Abstract
Histone variants and the associated post-translational modifications that govern the stemness of haematopoietic stem cells (HSCs) and differentiation thereof into progenitors (HSPCs) have not been well defined. H3.3 is a replication-independent H3 histone variant in mammalian systems that is enriched at both H3K4me3- and H3K27me3-marked bivalent genes as well as H3K9me3-marked endogenous retroviral repeats. Here we show that H3.3, but not its chaperone Hira, prevents premature HSC exhaustion and differentiation into granulocyte-macrophage progenitors. H3.3-null HSPCs display reduced expression of stemness and lineage-specific genes with a predominant gain of H3K27me3 marks at their promoter regions. Concomitantly, loss of H3.3 leads to a reduction of H3K9me3 marks at endogenous retroviral repeats, opening up binding sites for the interferon regulatory factor family of transcription factors, allowing the survival of rare, persisting H3.3-null HSCs. We propose a model whereby H3.3 maintains adult HSC stemness by safeguarding the delicate interplay between H3K27me3 and H3K9me3 marks, enforcing chromatin adaptability.
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Affiliation(s)
- Peipei Guo
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA. .,Fibrosis Research Center, Mount Sinai-National Jewish Respiratory Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Ying Liu
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,These authors contributed equally: Peipei Guo, Ying Liu
| | - Fuqiang Geng
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W. Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Xiaoyu Liu
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA.,Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Liangwen Zhong
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Raphael Lis
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA
| | - José Gabriel Barcia Durán
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Tomer Itkin
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Fanying Tang
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.,Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY, USA.,Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Tuo Zhang
- Weill Cornell Genomics Core Facility, New York, NY, USA
| | - Jenny Xiang
- Weill Cornell Genomics Core Facility, New York, NY, USA
| | - Koji Shido
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA
| | - Bi-sen Ding
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.,Fibrosis Research Center, Mount Sinai–National Jewish Respiratory Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Steven Z. Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shahin Rafii
- Department of Medicine, Division of Regenerative Medicine, Ansary Stem Cell Institute, Weill Cornell Medicine, New York, NY, USA.
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25
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Kudo H, Arakawa GY, Shirai S, Ogawa M, Shindo H, Hosaka M, Tokuoka M. New role of a histone chaperone, HirA: Involvement in kojic acid production associated with culture conditions in Aspergillusoryzae. J Biosci Bioeng 2021; 133:235-242. [PMID: 34952787 DOI: 10.1016/j.jbiosc.2021.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 10/29/2021] [Accepted: 12/05/2021] [Indexed: 10/19/2022]
Abstract
Kojic acid (KA) is a representative secondary metabolite of Aspergillus oryzae, but the underlying molecular mechanisms that regulate KA production are unknown. This study tried to find a genetic factor of KA production in A. oryzae, with a special focus on liquid cultures. We screened a gene predicted to encode HirA, a subunit of the histone chaperon, the HIR complex. A gene disruption strain of hirA showed decreased KA production in liquid culture, whereas it showed increased KA production in plate culture. We confirmed that a decrease/increase of KA production observed by hirA disruption was caused by altered expression of kojA and kojR. These observations suggested the regulatory role of histone chaperon in secondary metabolism in filamentous fungi. So far as we know, this report is the first showing that disruption of a gene resulted in the opposite effect on KA production in liquid and plate cultures in A. oryzae.
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Affiliation(s)
- Hayato Kudo
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Gen-Ya Arakawa
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Saya Shirai
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masahiro Ogawa
- Noda Institute for Scientific Research, 338 Noda, Noda, Chiba 278-0037, Japan
| | - Hitoshi Shindo
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masaru Hosaka
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masafumi Tokuoka
- Graduate School of Agriculture, Department of Fermentation Science and Technology, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan; Department of Fermentation Science, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.
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26
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Bouvier D, Ferrand J, Chevallier O, Paulsen MT, Ljungman M, Polo SE. Dissecting regulatory pathways for transcription recovery following DNA damage reveals a non-canonical function of the histone chaperone HIRA. Nat Commun 2021; 12:3835. [PMID: 34158510 PMCID: PMC8219801 DOI: 10.1038/s41467-021-24153-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
Transcription restart after a genotoxic challenge is a fundamental yet poorly understood process. Here, we dissect the interplay between transcription and chromatin restoration after DNA damage by focusing on the human histone chaperone complex HIRA, which is required for transcription recovery post UV. We demonstrate that HIRA is recruited to UV-damaged chromatin via the ubiquitin-dependent segregase VCP to deposit new H3.3 histones. However, this local activity of HIRA is dispensable for transcription recovery. Instead, we reveal a genome-wide function of HIRA in transcription restart that is independent of new H3.3 and not restricted to UV-damaged loci. HIRA coordinates with ASF1B to control transcription restart by two independent pathways: by stabilising the associated subunit UBN2 and by reducing the expression of the transcription repressor ATF3. Thus, HIRA primes UV-damaged chromatin for transcription restart at least in part by relieving transcription inhibition rather than by depositing new H3.3 as an activating bookmark.
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Affiliation(s)
- Déborah Bouvier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Juliette Ferrand
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Odile Chevallier
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France
| | - Michelle T Paulsen
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Sophie E Polo
- Epigenetics & Cell Fate Centre, UMR7216 CNRS, Université de Paris, Paris, France.
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27
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Smith R, Pickering SJ, Kopakaki A, Thong KJ, Anderson RA, Lin CJ. HIRA contributes to zygote formation in mice and is implicated in human 1PN zygote phenotype. Reproduction 2021; 161:697-707. [PMID: 33835048 PMCID: PMC8188263 DOI: 10.1530/rep-20-0636] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/08/2021] [Indexed: 11/08/2022]
Abstract
Elucidating the mechanisms underpinning fertilisation is essential to optimising IVF procedures. One of the critical steps involves paternal chromatin reprogramming, in which compacted sperm chromatin packed by protamines is removed by oocyte factors and new histones, including histone H3.3, are incorporated. HIRA is the main H3.3 chaperone governing this protamine-to-histone exchange. Failure of this step results in abnormally fertilised zygotes containing only one pronucleus (1PN), in contrast to normal two-pronuclei (2PN) zygotes. 1PN zygotes are frequently observed in IVF treatments, but the genotype-phenotype correlation remains elusive. We investigated the maternal functions of two other molecules of the HIRA complex, Cabin1 and Ubn1, in mouse. Loss-of-function Cabin1 and Ubn1 mouse models were developed: their zygotes displayed an abnormal 1PN zygote phenotype. We then studied human 1PN zygotes and found that the HIRA complex was absent in 1PN zygotes that lacked the male pronucleus. This shows that the role of the HIRA complex in male pronucleus formation potentially has coherence from mice to humans. Furthermore, rescue experiments in mouse showed that the abnormal 1PN phenotype derived from Hira mutants could be resolved by overexpression of HIRA. We have demonstrated that HIRA complex regulates male pronucleus formation in mice and is implicated in humans, that both CABIN1 and UBN1 components of the HIRA complex are equally essential for male pronucleus formation, and that rescue is feasible.
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Affiliation(s)
- Rowena Smith
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
| | - Sue J Pickering
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Anna Kopakaki
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - K J Thong
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Richard A Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
- Edinburgh Fertility and Reproductive Endocrine Centre, Simpson’s Centre for Reproductive Health, Edinburgh Royal Infirmary, Edinburgh, UK
| | - Chih-Jen Lin
- MRC Centre for Reproductive Health, University of Edinburgh, Queen’s Medical Research Institute, Edinburgh Bioquarter, Edinburgh, UK
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28
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Piette BL, Alerasool N, Lin ZY, Lacoste J, Lam MHY, Qian WW, Tran S, Larsen B, Campos E, Peng J, Gingras AC, Taipale M. Comprehensive interactome profiling of the human Hsp70 network highlights functional differentiation of J domains. Mol Cell 2021; 81:2549-2565.e8. [PMID: 33957083 DOI: 10.1016/j.molcel.2021.04.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/22/2022]
Abstract
Hsp70s comprise a deeply conserved chaperone family that has a central role in maintaining protein homeostasis. In humans, Hsp70 client specificity is provided by 49 different co-factors known as J domain proteins (JDPs). However, the cellular function and client specificity of JDPs have largely remained elusive. We have combined affinity purification-mass spectrometry (AP-MS) and proximity-dependent biotinylation (BioID) to characterize the interactome of all human JDPs and Hsp70s. The resulting network suggests specific functions for many uncharacterized JDPs, and we establish a role of conserved JDPs DNAJC9 and DNAJC27 in histone chaperoning and ciliogenesis, respectively. Unexpectedly, we find that the J domain of DNAJC27 but not of other JDPs can fully replace the function of endogenous DNAJC27, suggesting a previously unappreciated role for J domains themselves in JDP specificity. More broadly, our work expands the role of the Hsp70-regulated proteostasis network and provides a platform for further discovery of JDP-dependent functions.
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Affiliation(s)
- Benjamin L Piette
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Jessica Lacoste
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mandy Hiu Yi Lam
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Wesley Wei Qian
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Stephanie Tran
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Eric Campos
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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29
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Ray-Gallet D, Almouzni G. The Histone H3 Family and Its Deposition Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:17-42. [PMID: 33155135 DOI: 10.1007/978-981-15-8104-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.
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Affiliation(s)
- Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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30
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Wu H, Nakazawa T, Morimoto R, Sakamoto M, Honda Y. Targeted disruption of hir1 alters the transcriptional expression pattern of putative lignocellulolytic genes in the white-rot fungus Pleurotus ostreatus. Fungal Genet Biol 2021; 147:103507. [PMID: 33383191 DOI: 10.1016/j.fgb.2020.103507] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/28/2020] [Accepted: 12/22/2020] [Indexed: 11/16/2022]
Abstract
Pleurotus ostreatus is frequently used in molecular genetics and genomic studies on white-rot fungi because various molecular genetic tools and relatively well-annotated genome databases are available. To explore the molecular mechanisms underlying wood lignin degradation by P. ostreatus, we performed mutational analysis of a newly isolated mutant UVRM28 that exhibits decreased lignin-degrading ability on the beech wood sawdust medium. We identified that a mutation in the hir1 gene encoding a putative histone chaperone, which probably plays an important role in DNA replication-independent nucleosome assembly, is responsible for the mutant phenotype. The expression pattern of ligninolytic genes was altered in hir1 disruptants. The most highly expressed gene vp2 was significantly inactivated, whereas the expression of vp1 was remarkably upregulated (300-400 fold) at the transcription level. Conversely, many cellulolytic and xylanolytic genes were upregulated in hir1 disruptants. Chromatin immunoprecipitation analysis suggested that the histone modification status was altered in the 5'-upstream regions of some of the up- and down-regulated lignocellulolytic genes in hir1 disruptants compared with that in the 20b strain. Hence, our data provide new insights into the regulatory mechanisms of lignocellulolytic genes in P. ostreatus.
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Affiliation(s)
- Hongli Wu
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takehito Nakazawa
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Ryota Morimoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masahiro Sakamoto
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yoichi Honda
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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31
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Corpet A, Kleijwegt C, Roubille S, Juillard F, Jacquet K, Texier P, Lomonte P. PML nuclear bodies and chromatin dynamics: catch me if you can! Nucleic Acids Res 2020; 48:11890-11912. [PMID: 33068409 PMCID: PMC7708061 DOI: 10.1093/nar/gkaa828] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/15/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells compartmentalize their internal milieu in order to achieve specific reactions in time and space. This organization in distinct compartments is essential to allow subcellular processing of regulatory signals and generate specific cellular responses. In the nucleus, genetic information is packaged in the form of chromatin, an organized and repeated nucleoprotein structure that is a source of epigenetic information. In addition, cells organize the distribution of macromolecules via various membrane-less nuclear organelles, which have gathered considerable attention in the last few years. The macromolecular multiprotein complexes known as Promyelocytic Leukemia Nuclear Bodies (PML NBs) are an archetype for nuclear membrane-less organelles. Chromatin interactions with nuclear bodies are important to regulate genome function. In this review, we will focus on the dynamic interplay between PML NBs and chromatin. We report how the structure and formation of PML NBs, which may involve phase separation mechanisms, might impact their functions in the regulation of chromatin dynamics. In particular, we will discuss how PML NBs participate in the chromatinization of viral genomes, as well as in the control of specific cellular chromatin assembly pathways which govern physiological mechanisms such as senescence or telomere maintenance.
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Affiliation(s)
- Armelle Corpet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Constance Kleijwegt
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Simon Roubille
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Franceline Juillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Karine Jacquet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Pascale Texier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
| | - Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5310, INSERM U 1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Dynamics, Nuclear Domains, Virus F-69008, Lyon, France
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32
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Wei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2020; 184:76-91.e13. [PMID: 33147444 PMCID: PMC7574718 DOI: 10.1016/j.cell.2020.10.028] [Citation(s) in RCA: 341] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/11/2020] [Accepted: 10/15/2020] [Indexed: 12/17/2022]
Abstract
Identification of host genes essential for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection may reveal novel therapeutic targets and inform our understanding of coronavirus disease 2019 (COVID-19) pathogenesis. Here we performed genome-wide CRISPR screens in Vero-E6 cells with SARS-CoV-2, Middle East respiratory syndrome CoV (MERS-CoV), bat CoV HKU5 expressing the SARS-CoV-1 spike, and vesicular stomatitis virus (VSV) expressing the SARS-CoV-2 spike. We identified known SARS-CoV-2 host factors, including the receptor ACE2 and protease Cathepsin L. We additionally discovered pro-viral genes and pathways, including HMGB1 and the SWI/SNF chromatin remodeling complex, that are SARS lineage and pan-coronavirus specific, respectively. We show that HMGB1 regulates ACE2 expression and is critical for entry of SARS-CoV-2, SARS-CoV-1, and NL63. We also show that small-molecule antagonists of identified gene products inhibited SARS-CoV-2 infection in monkey and human cells, demonstrating the conserved role of these genetic hits across species. This identifies potential therapeutic targets for SARS-CoV-2 and reveals SARS lineage-specific and pan-CoV host factors that regulate susceptibility to highly pathogenic CoVs.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Peter C DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ruth E Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Wesley L Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madison S Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Vincent R Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Cameron O Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer S Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Madeleine C Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Renata B Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Neal G Ravindra
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Victor Gasque
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Fernando J de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ajinkya Patil
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kasopefoluwa Y Oguntuyo
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Yulia V Surovtseva
- Yale Center for Molecular Discovery, Yale University, West Haven, CT 06516, USA
| | - Robert C Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brett D Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA; Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - David van Dijk
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Matthew D Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT 06520, USA; Chemical Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - John G Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig B Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA.
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33
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Torné J, Ray-Gallet D, Boyarchuk E, Garnier M, Le Baccon P, Coulon A, Orsi GA, Almouzni G. Two HIRA-dependent pathways mediate H3.3 de novo deposition and recycling during transcription. Nat Struct Mol Biol 2020; 27:1057-1068. [PMID: 32895554 DOI: 10.1038/s41594-020-0492-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
Nucleosomes represent a challenge in regard to transcription. Histone eviction enables RNA polymerase II (RNAPII) progression through DNA, but compromises chromatin integrity. Here, we used the SNAP-tag system to distinguish new and old histones and monitor chromatin reassembly coupled to transcription in human cells. We uncovered a transcription-dependent loss of old histone variants H3.1 and H3.3. At transcriptionally active domains, H3.3 enrichment reflected both old H3.3 retention and new deposition. Mechanistically, we found that the histone regulator A (HIRA) chaperone is critical to processing both new and old H3.3 via different pathways. De novo H3.3 deposition is totally dependent on HIRA trimerization as well as on its partner ubinuclein 1 (UBN1), while antisilencing function 1 (ASF1) interaction with HIRA can be bypassed. By contrast, recycling of H3.3 requires HIRA but proceeds independently of UBN1 or HIRA trimerization and shows absolute dependency on ASF1-HIRA interaction. We propose a model whereby HIRA coordinates these distinct pathways during transcription to fine-tune chromatin states.
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Affiliation(s)
- Júlia Torné
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Ekaterina Boyarchuk
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Mickaël Garnier
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris, France
| | - Patricia Le Baccon
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Plateforme Imagerie PICT-IBiSA, Institut Curie, PSL Research University, Paris, France
| | - Antoine Coulon
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.,Institut Curie, PSL Research University, CNRS UMR168, Paris, France
| | - Guillermo A Orsi
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France. .,LBMC, Université de Lyon, ENS de Lyon, CNRS UMR5239, Université Claude Bernard Lyon 1, Lyon, France.
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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34
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Abstract
Nucleosome dynamics and properties are central to all forms of genomic activities. Among the core histones, H3 variants play a pivotal role in modulating nucleosome structure and function. Here, we focus on the impact of H3 variants on various facets of development. The deposition of the replicative H3 variant following DNA replication is essential for the transmission of the epigenomic information encoded in posttranscriptional modifications. Through this process, replicative H3 maintains cell fate while, in contrast, the replacement H3.3 variant opposes cell differentiation during early embryogenesis. In later steps of development, H3.3 and specialized H3 variants are emerging as new, important regulators of terminal cell differentiation, including neurons and gametes. The specific pathways that regulate the dynamics of the deposition of H3.3 are paramount during reprogramming events that drive zygotic activation and the initiation of a new cycle of development.
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Affiliation(s)
- Benjamin Loppin
- Laboratoire de Biologie et de Modélisation de la Cellule, CNRS UMR 5239, Ecole Normale Supérieure de Lyon, University of Lyon, F-69007 Lyon, France;
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria;
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35
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Wei J, Alfajaro MM, Hanna RE, DeWeirdt PC, Strine MS, Lu-Culligan WJ, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Gasque V, de Miguel F, Chen H, Oguntuyo K, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach B, Politi K, van Dijk D, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR screen reveals host genes that regulate SARS-CoV-2 infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.16.155101. [PMID: 32869025 PMCID: PMC7457610 DOI: 10.1101/2020.06.16.155101] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Identification of host genes essential for SARS-CoV-2 infection may reveal novel therapeutic targets and inform our understanding of COVID-19 pathogenesis. Here we performed a genome-wide CRISPR screen with SARS-CoV-2 and identified known SARS-CoV-2 host factors including the receptor ACE2 and protease Cathepsin L. We additionally discovered novel pro-viral genes and pathways including the SWI/SNF chromatin remodeling complex and key components of the TGF-β signaling pathway. Small molecule inhibitors of these pathways prevented SARS-CoV-2-induced cell death. We also revealed that the alarmin HMGB1 is critical for SARS-CoV-2 replication. In contrast, loss of the histone H3.3 chaperone complex sensitized cells to virus-induced death. Together this study reveals potential therapeutic targets for SARS-CoV-2 and highlights host genes that may regulate COVID-19 pathogenesis.
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Affiliation(s)
- Jin Wei
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ruth E. Hanna
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peter C. DeWeirdt
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Madison S. Strine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - William J. Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
| | - Shang-Min Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Vincent R. Graziano
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Cameron O. Schmitz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jennifer S. Chen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Madeleine C. Mankowski
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Renata B. Filler
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Fernando de Miguel
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Huacui Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Laura Abriola
- Yale Center for Molecular Discovery, Yale University, West Haven, CT, USA
| | | | - Robert C. Orchard
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Benhur Lee
- Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brett Lindenbach
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Katerina Politi
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - David van Dijk
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Matthew D. Simon
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Chemical Biology Institute, Yale University, West Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - John G. Doench
- Genetic Perturbation Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
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36
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Liang J, Zhao H, Diplas BH, Liu S, Liu J, Wang D, Lu Y, Zhu Q, Wu J, Wang W, Yan H, Zeng YX, Wang X, Jiao Y. Genome-Wide CRISPR-Cas9 Screen Reveals Selective Vulnerability of ATRX-Mutant Cancers to WEE1 Inhibition. Cancer Res 2019; 80:510-523. [PMID: 31551363 DOI: 10.1158/0008-5472.can-18-3374] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/28/2019] [Accepted: 09/17/2019] [Indexed: 11/16/2022]
Abstract
The tumor suppressor gene ATRX is frequently mutated in a variety of tumors including gliomas and liver cancers, which are highly unresponsive to current therapies. Here, we performed a genome-wide synthetic lethal screen, using CRISPR-Cas9 genome editing, to identify potential therapeutic targets specific for ATRX-mutated cancers. In isogenic hepatocellular carcinoma (HCC) cell lines engineered for ATRX loss, we identified 58 genes, including the checkpoint kinase WEE1, uniquely required for the cell growth of ATRX null cells. Treatment with the WEE1 inhibitor AZD1775 robustly inhibited the growth of several ATRX-deficient HCC cell lines in vitro, as well as xenografts in vivo. The increased sensitivity to the WEE1 inhibitor was caused by accumulated DNA damage-induced apoptosis. AZD1775 also selectively inhibited the proliferation of patient-derived primary cell lines from gliomas with naturally occurring ATRX mutations, indicating that the synthetic lethal relationship between WEE1 and ATRX could be exploited in a broader spectrum of human tumors. As WEE1 inhibitors have been investigated in several phase II clinical trials, our discovery provides the basis for an easily clinically testable therapeutic strategy specific for cancers deficient in ATRX. SIGNIFICANCE: ATRX-mutant cancer cells depend on WEE1, which provides a basis for therapeutically targeting WEE1 in ATRX-deficient cancers.See related commentary by Cole, p. 375.
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Affiliation(s)
- Junbo Liang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hong Zhao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bill H Diplas
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Song Liu
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China
| | - Jianmei Liu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dingding Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yan Lu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Qing Zhu
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
| | - Jiayu Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Wenjia Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hai Yan
- The Preston Robert Tisch Brain Tumor Center at Duke, Pediatric Brain Tumor Foundation Institute at Duke, and Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Yi-Xin Zeng
- Department of Experimental Research, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong Province, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China. .,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Ricketts MD, Dasgupta N, Fan J, Han J, Gerace M, Tang Y, Black BE, Adams PD, Marmorstein R. The HIRA histone chaperone complex subunit UBN1 harbors H3/H4- and DNA-binding activity. J Biol Chem 2019; 294:9239-9259. [PMID: 31040182 DOI: 10.1074/jbc.ra119.007480] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 04/01/2019] [Indexed: 02/04/2023] Open
Abstract
The HIRA histone chaperone complex is composed of the proteins HIRA, UBN1, and CABIN1 and cooperates with the histone chaperone ASF1a to specifically bind and deposit H3.3/H4 into chromatin. We recently reported that the UBN1 Hpc2-related domain (HRD) specifically binds to H3.3/H4 over H3.1/H4. However, the mechanism for HIRA complex deposition of H3.3/H4 into nucleosomes remains unclear. Here, we characterize a central region of UBN1 (UBN1 middle domain) that is evolutionarily conserved and predicted to have helical secondary structure. We report that the UBN1 middle domain has dimer formation activity and binds to H3/H4 in a manner that does not discriminate between H3.1 and H3.3. We additionally identify a nearby DNA-binding domain in UBN1, located between the UBN1 HRD and middle domain, which binds DNA through electrostatic contacts involving several conserved lysine residues. Together, these observations suggest a mechanism for HIRA-mediated H3.3/H4 deposition whereby UBN1 associates with DNA and dimerizes to mediate formation of an (H3.3/H4)2 heterotetramer prior to chromatin deposition.
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Affiliation(s)
- M Daniel Ricketts
- From the Department of Biochemistry and Biophysics and.,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Nirmalya Dasgupta
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Jiayi Fan
- From the Department of Biochemistry and Biophysics and
| | - Joseph Han
- From the Department of Biochemistry and Biophysics and.,the Department of Chemistry Graduate Group and
| | - Morgan Gerace
- From the Department of Biochemistry and Biophysics and
| | - Yong Tang
- the Wistar Institute, Philadelphia, Pennsylvania 19104, and
| | - Ben E Black
- From the Department of Biochemistry and Biophysics and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Peter D Adams
- the Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037
| | - Ronen Marmorstein
- From the Department of Biochemistry and Biophysics and .,the Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,the Department of Chemistry Graduate Group and.,the Wistar Institute, Philadelphia, Pennsylvania 19104, and.,the Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
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38
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Spirkoski J, Shah A, Reiner AH, Collas P, Delbarre E. PML modulates H3.3 targeting to telomeric and centromeric repeats in mouse fibroblasts. Biochem Biophys Res Commun 2019; 511:882-888. [PMID: 30850162 DOI: 10.1016/j.bbrc.2019.02.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/16/2019] [Indexed: 10/27/2022]
Abstract
Targeted deposition of histone variant H3.3 into chromatin is paramount for proper regulation of chromatin integrity, particularly in heterochromatic regions including repeats. We have recently shown that the promyelocytic leukemia (PML) protein prevents H3.3 from being deposited in large heterochromatic PML-associated domains (PADs). However, to what extent PML modulates H3.3 loading on chromatin in other areas of the genome remains unexplored. Here, we examined the impact of PML on targeting of H3.3 to genes and repeat regions that reside outside PADs. We show that loss of PML increases H3.3 deposition in subtelomeric, telomeric, pericentric and centromeric repeats in mouse embryonic fibroblasts, while other repeat classes are not affected. Expression of major satellite, minor satellite and telomeric non-coding transcripts is altered in Pml-null cells. In particular, telomeric Terra transcripts are strongly upregulated, in concordance with a marked reduction in H4K20me3 at these sites. Lastly, for most genes H3.3 enrichment or gene expression outcomes are independent of PML. Our data argue towards the importance of a PML-H3.3 axis in preserving a heterochromatin state at centromeres and telomeres.
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Affiliation(s)
- Jane Spirkoski
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
| | - Akshay Shah
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway
| | - Andrew H Reiner
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway; Oslo Center for Biostatistics and Epidemiology, Research Support Services, Oslo University Hospital, Oslo, Norway
| | - Philippe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway; Norwegian Center for Stem Cell Research, Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424, Oslo, Norway.
| | - Erwan Delbarre
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, PO Box 1112 Blindern, 0317, Oslo, Norway.
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Xiong C, Wen Z, Yu J, Chen J, Liu CP, Zhang X, Chen P, Xu RM, Li G. UBN1/2 of HIRA complex is responsible for recognition and deposition of H3.3 at cis-regulatory elements of genes in mouse ES cells. BMC Biol 2018; 16:110. [PMID: 30285846 PMCID: PMC6171237 DOI: 10.1186/s12915-018-0573-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/06/2018] [Indexed: 01/08/2023] Open
Abstract
Background H3.3 is an ancient and conserved H3 variant and plays essential roles in transcriptional regulation. HIRA complex, which is composed of HIRA, UBN1 or UBN2, and Cabin1, is a H3.3 specific chaperone complex. However, it still remains largely uncharacterized how HIRA complex specifically recognizes and deposits H3.3 to the chromatin, such as promoters and enhancers. Results In this study, we demonstrate that the UBN1 or UBN2 subunit is mainly responsible for specific recognition and direct binding of H3.3 by the HIRA complex. While the HIRA subunit can enhance the binding affinity of UBN1 toward H3.3, Cabin1 subunit cannot. We also demonstrate that both Ala87 and Gly90 residues of H3.3 are required and sufficient for the specific recognition and binding by UBN1. ChIP-seq studies reveal that two independent HIRA complexes (UBN1-HIRA and UBN2-HIRA) can cooperatively deposit H3.3 to cis-regulatory regions, including active promoters and active enhancers in mouse embryonic stem (mES) cells. Importantly, disruption of histone chaperone activities of UBN1 and UBN2 by FID/AAA mutation results in the defect of H3.3 deposition at promoters of developmental genes involved in neural differentiation, and subsequently causes the failure of activation of these genes during neural differentiation of mES cells. Conclusion Together, our results provide novel insights into the mechanism by which the HIRA complex specifically recognizes and deposits H3.3 at promoters and enhancers of developmental genes, which plays a critical role in neural differentiation of mES cells. Electronic supplementary material The online version of this article (10.1186/s12915-018-0573-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chaoyang Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zengqi Wen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Yu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaodong Zhang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ping Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Promyelocytic leukemia (PML) nuclear bodies (NBs) induce latent/quiescent HSV-1 genomes chromatinization through a PML NB/Histone H3.3/H3.3 Chaperone Axis. PLoS Pathog 2018; 14:e1007313. [PMID: 30235352 PMCID: PMC6168178 DOI: 10.1371/journal.ppat.1007313] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/02/2018] [Accepted: 08/31/2018] [Indexed: 12/31/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) latency establishment is tightly controlled by promyelocytic leukemia (PML) nuclear bodies (NBs) (or ND10), although their exact contribution is still elusive. A hallmark of HSV-1 latency is the interaction between latent viral genomes and PML NBs, leading to the formation of viral DNA-containing PML NBs (vDCP NBs), and the complete silencing of HSV-1. Using a replication-defective HSV-1-infected human primary fibroblast model reproducing the formation of vDCP NBs, combined with an immuno-FISH approach developed to detect latent/quiescent HSV-1, we show that vDCP NBs contain both histone H3.3 and its chaperone complexes, i.e., DAXX/ATRX and HIRA complex (HIRA, UBN1, CABIN1, and ASF1a). HIRA also co-localizes with vDCP NBs present in trigeminal ganglia (TG) neurons from HSV-1-infected wild type mice. ChIP and Re-ChIP show that vDCP NBs-associated latent/quiescent viral genomes are chromatinized almost exclusively with H3.3 modified on its lysine (K) 9 by trimethylation, consistent with an interaction of the H3.3 chaperones with multiple viral loci and with the transcriptional silencing of HSV-1. Only simultaneous inactivation of both H3.3 chaperone complexes has a significant impact on the deposition of H3.3 on viral genomes, suggesting a compensation mechanism. In contrast, the sole depletion of PML significantly impacts the chromatinization of the latent/quiescent viral genomes with H3.3 without any overall replacement with H3.1. vDCP NBs-associated HSV-1 genomes are not definitively silenced since the destabilization of vDCP NBs by ICP0, which is essential for HSV-1 reactivation in vivo, allows the recovery of a transcriptional lytic program and the replication of viral genomes. Consequently, the present study demonstrates a specific chromatin regulation of vDCP NBs-associated latent/quiescent HSV-1 through an H3.3-dependent HSV-1 chromatinization involving the two H3.3 chaperones DAXX/ATRX and HIRA complexes. Additionally, the study reveals that PML NBs are major actors in latent/quiescent HSV-1 H3.3 chromatinization through a PML NB/histone H3.3/H3.3 chaperone axis. An understanding of the molecular mechanisms contributing to the persistence of a virus in its host is essential to be able to control viral reactivation and its associated diseases. Herpes simplex virus 1 (HSV-1) is a human pathogen that remains latent in the PNS and CNS of the infected host. The latency is unstable, and frequent reactivations of the virus are responsible for PNS and CNS pathologies. It is thus crucial to understand the physiological, immunological and molecular levels of interplay between latent HSV-1 and the host. Promyelocytic leukemia (PML) nuclear bodies (NBs) control viral infections by preventing the onset of lytic infection. In previous studies, we showed a major role of PML NBs in favoring the establishment of a latent state for HSV-1. A hallmark of HSV-1 latency establishment is the formation of PML NBs containing the viral genome, which we called “viral DNA-containing PML NBs” (vDCP NBs). The genome entrapped in the vDCP NBs is transcriptionally silenced. This naturally occurring latent/quiescent state could, however, be transcriptionally reactivated. Therefore, understanding the role of PML NBs in controlling the establishment of HSV-1 latency and its reactivation is essential to design new therapeutic approaches based on the prevention of viral reactivation.
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Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit. Nat Commun 2018; 9:3103. [PMID: 30082790 PMCID: PMC6078998 DOI: 10.1038/s41467-018-05581-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 07/11/2018] [Indexed: 02/07/2023] Open
Abstract
The HIRA histone chaperone complex deposits the histone variant H3.3 onto chromatin in a DNA synthesis-independent manner. It comprises three identified subunits, HIRA, UBN1 and CABIN1, however the functional oligomerization state of the complex has not been investigated. Here we use biochemical and crystallographic analysis to show that the HIRA subunit forms a stable homotrimer that binds two subunits of CABIN1 in vitro. A HIRA mutant that is defective in homotrimer formation interacts less efficiently with CABIN1, is not enriched at DNA damage sites upon UV irradiation and cannot rescue new H3.3 deposition in HIRA knockout cells. The structural homology with the homotrimeric replisome component Ctf4/AND-1 enables the drawing of parallels and discussion of the functional importance of the homotrimerization state of the HIRA subunit. The HIRA histone chaperone complex is involved in the deposition of the histone variant H3.3. Here the authors, by using biochemical and crystallographic approaches, report the homotrimerization of the HIRA subunit which is critical for the functional activity of the complex.
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42
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The plant-specific histone residue Phe41 is important for genome-wide H3.1 distribution. Nat Commun 2018; 9:630. [PMID: 29434220 PMCID: PMC5809374 DOI: 10.1038/s41467-018-02976-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 01/11/2018] [Indexed: 12/21/2022] Open
Abstract
The dynamic incorporation of histone variants influences chromatin structure and many biological processes. In Arabidopsis, the canonical variant H3.1 differs from H3.3 in four residues, one of which (H3.1Phe41) is unique and conserved in plants. However, its evolutionary significance remains unclear. Here, we show that Phe41 first appeared in H3.1 in ferns and became stable during land plant evolution. Unlike H3.1, which is specifically enriched in silent regions, H3.1F41Y variants gain ectopic accumulation at actively transcribed regions. Reciprocal tail and core domain swap experiments between H3.1 and H3.3 show that the H3.1 core, while necessary, is insufficient to restrict H3.1 to silent regions. We conclude that the vascular-plant-specific Phe41 is critical for H3.1 genomic distribution and may act collaboratively with the H3.1 core to regulate deposition patterns. This study reveals that Phe41 may have evolved to provide additional regulation of histone deposition in plants. The canonical histone variant H3.1 of vascular plants contains a conserved Phe residue at position 41 that is unique to the plant kingdom. Here, Lu et al. provide evidence that H3.1Phe41 acts collaboratively with the H3.1 core domain to restrict H3.1 deposition to silent regions of the genome.
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43
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Rai TS, Glass M, Cole JJ, Rather MI, Marsden M, Neilson M, Brock C, Humphreys IR, Everett RD, Adams PD. Histone chaperone HIRA deposits histone H3.3 onto foreign viral DNA and contributes to anti-viral intrinsic immunity. Nucleic Acids Res 2017; 45:11673-11683. [PMID: 28981850 PMCID: PMC5691367 DOI: 10.1093/nar/gkx771] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 08/14/2017] [Accepted: 09/08/2017] [Indexed: 12/22/2022] Open
Abstract
The HIRA histone chaperone complex deposits histone H3.3 into nucleosomes in a DNA replication- and sequence-independent manner. As herpesvirus genomes enter the nucleus as naked DNA, we asked whether the HIRA chaperone complex affects herpesvirus infection. After infection of primary cells with HSV or CMV, or transient transfection with naked plasmid DNA, HIRA re-localizes to PML bodies, sites of cellular anti-viral activity. HIRA co-localizes with viral genomes, binds to incoming viral and plasmid DNAs and deposits histone H3.3 onto these. Anti-viral interferons (IFN) specifically induce HIRA/PML co-localization at PML nuclear bodies and HIRA recruitment to IFN target genes, although HIRA is not required for IFN-inducible expression of these genes. HIRA is, however, required for suppression of viral gene expression, virus replication and lytic infection and restricts murine CMV replication in vivo. We propose that the HIRA chaperone complex represses incoming naked viral DNAs through chromatinization as part of intrinsic cellular immunity.
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Affiliation(s)
- Taranjit Singh Rai
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, PA1 2BE, Scotland
- Beatson Institute for Cancer Research, Glasgow, Scotland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - Mandy Glass
- Institute of Biomedical and Environmental Health Research, University of the West of Scotland, Paisley, PA1 2BE, Scotland
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - John J. Cole
- Beatson Institute for Cancer Research, Glasgow, Scotland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - Mohammad I. Rather
- Beatson Institute for Cancer Research, Glasgow, Scotland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - Morgan Marsden
- Cardiff Institute of Infection & Immunity, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | | | - Claire Brock
- Beatson Institute for Cancer Research, Glasgow, Scotland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - Ian R. Humphreys
- Cardiff Institute of Infection & Immunity, Cardiff University, Cardiff, Wales, CF14 4XN, UK
| | - Roger D. Everett
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, G61 1QH, Scotland
| | - Peter D. Adams
- Beatson Institute for Cancer Research, Glasgow, Scotland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, Scotland
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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44
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Bano D, Piazzesi A, Salomoni P, Nicotera P. The histone variant H3.3 claims its place in the crowded scene of epigenetics. Aging (Albany NY) 2017; 9:602-614. [PMID: 28284043 PMCID: PMC5391221 DOI: 10.18632/aging.101194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/26/2017] [Indexed: 12/16/2022]
Abstract
Histones are evolutionarily conserved DNA-binding proteins. As scaffolding molecules, they significantly regulate the DNA packaging into the nucleus of all eukaryotic cells. As docking units, they influence the recruitment of the transcriptional machinery, thus establishing unique gene expression patterns that ultimately promote different biological outcomes. While canonical histones H3.1 and H3.2 are synthetized and loaded during DNA replication, the histone variant H3.3 is expressed and deposited into the chromatin throughout the cell cycle. Recent findings indicate that H3.3 replaces the majority of canonical H3 in non-dividing cells, reaching almost saturation levels in a time-dependent manner. Consequently, H3.3 incorporation and turnover represent an additional layer in the regulation of the chromatin landscape during aging. In this respect, work from our group and others suggest that H3.3 plays an important function in age-related processes throughout evolution. Here, we summarize the current knowledge on H3.3 biology and discuss the implications of its aberrant dynamics in the establishment of cellular states that may lead to human pathology. Critically, we review the importance of H3.3 turnover as part of epigenetic events that influence senescence and age-related processes. We conclude with the emerging evidence that H3.3 is required for proper neuronal function and brain plasticity.
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Affiliation(s)
- Daniele Bano
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Antonia Piazzesi
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Paolo Salomoni
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Pierluigi Nicotera
- German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
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45
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Warren C, Shechter D. Fly Fishing for Histones: Catch and Release by Histone Chaperone Intrinsically Disordered Regions and Acidic Stretches. J Mol Biol 2017; 429:2401-2426. [PMID: 28610839 DOI: 10.1016/j.jmb.2017.06.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 01/21/2023]
Abstract
Chromatin is the complex of eukaryotic DNA and proteins required for the efficient compaction of the nearly 2-meter-long human genome into a roughly 10-micron-diameter cell nucleus. The fundamental repeating unit of chromatin is the nucleosome: 147bp of DNA wrapped about an octamer of histone proteins. Nucleosomes are stable enough to organize the genome yet must be dynamically displaced and reassembled to allow access to the underlying DNA for transcription, replication, and DNA damage repair. Histone chaperones are a non-catalytic group of proteins that are central to the processes of nucleosome assembly and disassembly and thus the fluidity of the ever-changing chromatin landscape. Histone chaperones are responsible for binding the highly basic histone proteins, shielding them from non-specific interactions, facilitating their deposition onto DNA, and aiding in their eviction from DNA. Although most histone chaperones perform these common functions, recent structural studies of many different histone chaperones reveal that there are few commonalities in their folds. Importantly, sequence-based predictions show that histone chaperones are highly enriched in intrinsically disordered regions (IDRs) and acidic stretches. In this review, we focus on the molecular mechanisms underpinning histone binding, selectivity, and regulation of these highly dynamic protein regions. We highlight new evidence suggesting that IDRs are often critical for histone chaperone function and play key roles in chromatin assembly and disassembly pathways.
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Affiliation(s)
- Christopher Warren
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
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46
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Zhu R, Iwabuchi M, Ohsumi K. The WD40 Domain of HIRA Is Essential for RI-nucleosome Assembly in Xenopus Egg Extracts. Cell Struct Funct 2017; 42:37-48. [PMID: 28381790 DOI: 10.1247/csf.17001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Histone chaperones are a group of histone-binding proteins that facilitate the assembly of nucleosomes, the fundamental structural units of chromatin in eukaryotes. In nucleosome assembly, deposition of a histone H3-H4 tetramer onto DNA is the first and critical step, which is mediated by the histone chaperones HIRA and CAF-1. HIRA and CAF-1 are reportedly involved in DNA replication independent (RI) and replication coupled nucleosome assembly, respectively. However, the mechanisms by which they mediate histone deposition remain unclear. In this study, we focused on the mechanism by which HIRA induces RI-nucleosome assembly. We looked for HIRA domains that are required for nucleosome assembly and its localization to chromatin. We used cell-free extracts from Xenopus eggs that carry out RI-nucleosome assembly of plasmid DNA. We confirmed that HIRA formed stable complexes with Asf1, another histone H3-H4 chaperone, and the HIRA-Asf1 complex was solely responsible for RI-nucleosome assembly in egg extracts. We further demonstrated that the HIRA N-terminus containing the WD40 domain, which comprises seven WD40 repeats, and the B domain, to which Asf1 binds, were essential for RI-nucleosome assembly; the three WD40 repeats from the N-terminus were especially critical. Using egg extracts that reproduce nuclear formation accompanying the duplication of chromatin, we also demonstrated that the Hir domain was indispensable for the binding of HIRA to chromatin. Thus, the WD40 and B domains are the core elements for inducing RI-nucleosome assembly. Hir domain regulates the binding to chromatin. Based on these findings, similarities and differences between HIRA and CAF-1 are discussed.
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Affiliation(s)
- Ruibin Zhu
- Group of Developmental Cell Biology, Graduate School of Science, Nagoya University
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47
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A Molecular Prospective for HIRA Complex Assembly and H3.3-Specific Histone Chaperone Function. J Mol Biol 2016; 429:1924-1933. [PMID: 27871933 DOI: 10.1016/j.jmb.2016.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/24/2022]
Abstract
Incorporation of variant histone sequences, in addition to post-translational modification of histones, serves to modulate the chromatin environment. Different histone chaperone proteins mediate the storage and chromatin deposition of variant histones. Although the two non-centromeric histone H3 variants, H3.1 and H3.3, differ by only 5 aa, replacement of histone H3.1 with H3.3 can modulate the transcription for highly expressed and developmentally required genes, lead to the formation of repressive heterochromatin, or aid in DNA and chromatin repair. The human histone cell cycle regulator (HIRA) complex composed of HIRA, ubinuclein-1, CABIN1, and transiently anti-silencing function 1, forms one of the two complexes that bind and deposit H3.3/H4 into chromatin. A number of recent biochemical and structural studies have revealed important details underlying how these proteins assemble and function together as a multiprotein H3.3-specific histone chaperone complex. Here, we present a review of existing data and present a new model for the assembly of the HIRA complex and for the HIRA-mediated incorporation of H3.3/H4 into chromatin.
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Abstract
PURPOSE OF REVIEW Cell senescence is a major process regulating tissue mass, architecture and function, and underlies many diseases of ageing. Recent studies have elucidated some of the regulatory pathways leading to cell senescence, and senescence has also been found in the vasculature. However, assessment of cell senescence is problematic, and the effects of vascular cell senescence are in most cases unproven. The present article will review how senescence is assessed, how it is regulated, where senescence has been described, and the role of cell senescence in atherosclerosis. RECENT FINDINGS Senescence results in expression of multiple proteins, both intracellular and secreted. However, to date, none of these are specific for senescence, and multiple markers must be used together for positive identification. Despite these shortfalls, cell senescence is detectable in the vasculature in ageing and in human atherosclerosis, and recent studies in mice have indicated that cell senescence promotes both atherogenesis and multiple features of 'vulnerable' lesions in advanced atherosclerotic plaques. SUMMARY The almost ubiquitous presence of cell senescence in atherosclerosis and the fundamental role of senescence in regulating plaque development and stability suggest that prevention or amelioration of senescence in atherosclerosis is a viable therapeutic target.
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Affiliation(s)
- Abel Martin Garrido
- Division of Cardiovascular Medicine, University of Cambridge, Box 110, Addenbrooke's Centre for Clinical Investigation, Addenbrooke's Hospital, Cambridge, UK
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Robin JD, Magdinier F. Physiological and Pathological Aging Affects Chromatin Dynamics, Structure and Function at the Nuclear Edge. Front Genet 2016; 7:153. [PMID: 27602048 PMCID: PMC4993774 DOI: 10.3389/fgene.2016.00153] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 08/08/2016] [Indexed: 01/29/2023] Open
Abstract
Lamins are intermediate filaments that form a complex meshwork at the inner nuclear membrane. Mammalian cells express two types of Lamins, Lamins A/C and Lamins B, encoded by three different genes, LMNA, LMNB1, and LMNB2. Mutations in the LMNA gene are associated with a group of phenotypically diverse diseases referred to as laminopathies. Lamins interact with a large number of binding partners including proteins of the nuclear envelope but also chromatin-associated factors. Lamins not only constitute a scaffold for nuclear shape, rigidity and resistance to stress but also contribute to the organization of chromatin and chromosomal domains. We will discuss here the impact of A-type Lamins loss on alterations of chromatin organization and formation of chromatin domains and how disorganization of the lamina contributes to the patho-physiology of premature aging syndromes.
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Affiliation(s)
- Jérôme D Robin
- IRCAN, CNRS UMR 7284/INSERM U1081, Faculté de Médecine Nice, France
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Differential regulation of the histone chaperone HIRA during muscle cell differentiation by a phosphorylation switch. Exp Mol Med 2016; 48:e252. [PMID: 27515126 PMCID: PMC5007640 DOI: 10.1038/emm.2016.68] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/19/2016] [Accepted: 03/02/2016] [Indexed: 01/05/2023] Open
Abstract
Replication-independent incorporation of variant histone H3.3 has a profound impact on chromatin function and numerous cellular processes, including the differentiation of muscle cells. The histone chaperone HIRA and H3.3 have essential roles in MyoD regulation during myoblast differentiation. However, the precise mechanism that determines the onset of H3.3 deposition in response to differentiation signals is unclear. Here we show that HIRA is phosphorylated by Akt kinase, an important signaling modulator in muscle cells. By generating a phosphospecific antibody, we found that a significant amount of HIRA was phosphorylated in myoblasts. The phosphorylation level of HIRA and the occupancy of phosphorylated protein on muscle genes gradually decreased during cellular differentiation. Remarkably, the forced expression of the phosphomimic form of HIRA resulted in reduced H3.3 deposition and suppressed the activation of muscle genes in myotubes. Our data show that HIRA phosphorylation limits the expression of myogenic genes, while the dephosphorylation of HIRA is required for proficient H3.3 deposition and gene activation, demonstrating that the phosphorylation switch is exploited to modulate HIRA/H3.3-mediated muscle gene regulation during myogenesis.
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